Research Output 2002 2019

2015

Natalie 2.0: Sparse Global Network Alignment as a Special Case of Quadratic Assignment

El-Kebir, M., Heringa, J. & Klau, G. W., 2015, In : Algorithms. 8, 4, p. 1035-1051

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Quadratic Assignment
Alignment
Topology
Quadratic Assignment Problem
Molecular interactions

NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL

May, A., Abeln, S., Buijs, M. J., Heringa, J., Crielaard, W. & Brandt, B. W., 2015, In : Nucleic Acids Research.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Microbial Genetics
Genetic Markers
Sequence Analysis
High-Throughput Nucleotide Sequencing
Metagenomics

On the fixed parameter tractability and approximability of the minimum error correction problem

Bonizzoni, P., Dondi, R., Klau, G. W., Pirola, Y., Pisanti, N. & Zaccaria, S., 2015, In : Lecture Notes in Computer Science. p. 100-113

Research output: Contribution to JournalArticleAcademicpeer-review

On tree-constrained matchings and generalizations

Canzar, S., Elbassioni, K., Klau, G. W. & Mestre, J., 2015, In : Algorithmica. 71, 1, p. 98-119

Research output: Contribution to JournalArticleAcademicpeer-review

Bipartite Matching
Matching Problem
Bipartite Graph
Generalization

Quantifying the Displacement of Mismatches in Multiple Sequence Alignment Benchmarks

van der Velde, A., Bawono, P., Abeln, S. & Heringa, J., 2015, In : PLoS ONE. 10, 5

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Benchmarking
Sequence Alignment
sequence alignment
methodology
case studies

SCRY: Enabling quantitative reasoning in SPARQL queries

Stringer, B., Meroño-Peñuela, A., Loizou, A., Abeln, S. & Heringa, J., 2015, In : CEUR Workshop Proceedings. 1546, p. 214-215 2 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Sequence specificity between interacting and non-interacting homologs identifies interface residues - a homodimer and monomer use case

Hou, Q., Dutilh, B. E., Huynen, M. A., Heringa, J. & Feenstra, K. A., 8 Oct 2015, In : BMC Bioinformatics. 16, p. 325-325

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Use Case
Specificity
Monomers
Proteins
Protein-protein Interaction

The Hydrophobic Temperature Dependence of Amino Acids Directly Calculated from Protein Structures

van Dijk, E., Hoogeveen, A. & Abeln, S., 1 May 2015, In : PLoS Computational Biology. 11, 5, e1004277.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Protein Structure
protein structure
Temperature Dependence
Amino Acids
Amino acids

To SCRY Linked Data: Extending SPARQL the Easy Way

Stringer, B., Meroño-Peñuela, A., Loizou, A., Abeln, S. & Heringa, J., 2015, In : CEUR Workshop Proceedings. 1501, p. 8-14 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
Statistical tests
Application programming interfaces (API)
Interoperability
Testing

Using bioconductor package BiGGR for metabolic flux estimation based on gene expression changes in brain.

Gavai, A. K., Supandi, F., Hettling, H., Murell, P., Leunissen, J. A. M. & van Beek, J. H. G. M., 2015, In : PLoS ONE. 10, 3, e0119016.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Gene expression
Systems Biology
Brain
Databases
Fluxes

Weighted haplotype assembly for future-generation sequencing reads

Patterson, M. D., Marschall, T., Pisanti, N., van Iersel, L. J. J., Stougie, L., Klau, G. W. & Schönhuth, A., 2015, In : Journal of Computational Biology. 22, 6, p. 498-509

Research output: Contribution to JournalArticleAcademicpeer-review

Haplotype
Social Responsibility
Nucleotides
Polymorphism
Haplotypes

xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model

El-Kebir, M., Soueidan, H., Hume, T., Beisser, D., Dittrich, M., Müller, T., Blin, G., Heringa, J., Nikolski, M., Wessels, L. F. A. & Klau, G. W., 1 Oct 2015, In : Bioinformatics. 31, 19, p. 3147-3155 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

T-cells
Conservation
Mining
Genes
Module
2014

Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins

May, A., Pool, R., van Dijk, E., Bijlard, J., Abeln, S., Heringa, J. & Feenstra, K. A., 1 Feb 2014, In : Bioinformatics. 30, 3, p. 326-34 9 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Atomistic Simulation
Free energy
Free Energy
Energy barriers
Proteins

Exact protein structure classification using the maximum contact map overlap metric

Wohlers, I., Le Boudic-Jamin, M., Djidjev, H., Klau, G. W. & Andonov, R., 2014, In : Lecture Notes in Computer Science. 8542, p. 262-273

Research output: Contribution to JournalArticleAcademicpeer-review

eXamine: Exploring annotated modules in networks

Dinkla, K., El-Kebir, M., Bucur, C. I., Siderius, M., Smit, M. J., Westenberg, M. A. & Klau, G. W., 2014, In : BMC Bioinformatics. 15, 201

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Molecular Sequence Annotation
Electric network analysis
G-Protein-Coupled Receptors
Proteins
Module

Functional module search in protein networks based on semantic similarity improves the analydsis of proteomics data

Boyanova, D., Nilla, S., Klau, G. W., Dandekar, T., Müller, T. & Dittrich, M., 2014, In : Molecular and Cellular Proteomics. 13, p. 1877-1889

Research output: Contribution to JournalArticleAcademicpeer-review

Semantics
Proteomics
Proteome
Proteins
Blood

NatalieQ: a web server for protein-protein interaction network querying

El-Kebir, M., Brandt, B. W., Heringa, J. & Klau, G. W., 2014, In : BMC Systems Biology. 8, 40, p. 1-7 7 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Protein Interaction Maps
Protein Interaction Networks
Web Server
Protein-protein Interaction
Alignment

Petri nets are a biologist's best friend

Bonzanni, N., Feenstra, K. A., Fokkink, W. J. & Heringa, J., 2014, Formal Methods in Macro-Biology: First International Conference, FMMB 2014, Nouméa, New Caledonia, September 22-24, 2014. Proceedings. Springer/Verlag, p. 102-116 15 p. (Lecture Notes in Computer Science; vol. 8738)( Lecture Notes in Bioinformatics book sub series (LNBI); vol. 8738).

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

File
Concurrency
Petri nets
Petri Nets
Cell Differentiation
Stem Cells

PRALINE: a versatile multiple sequence alignment toolkit.

Bawono, P. & Heringa, J., 2014, In : Methods in Molecular Biology. 10709, p. 245-262

Research output: Contribution to JournalArticleAcademicpeer-review

Sequence Alignment
Publications
Proteins

Scientific report: Training workshop interdisciplinary life sciences

Akudibillah, G., Boas, S. E. M., Carreres, B. M., Dallinga, M., van Dijk, A-J., Gupta, S. K., Hunt, A., Jacobsen, A., Kasbawati, K., Merks, R. R. M. H., Molenaar, J., Overal, G. G. B., Palm, M., Perenboom, M. J. L., Prasad, M., Reijnders, M., Rens, E. G., Ryback, B. M., Scheider, L., Srivastava, M. & 3 othersWillemsen, M. A. M., Wu, X. & Zagaris, A., 2014, In : PeerJ.

Research output: Contribution to JournalArticleAcademic

Open Access

Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations.

May, A., Abeln, S., Crielaard, W., Heringa, J. & Brandt, B. W., 2014, In : Bioinformatics. 30, p. 1530-1538

Research output: Contribution to JournalArticleAcademicpeer-review

Taxonomies
Taxonomy
Ribosomal DNA
Cluster Analysis
Preprocessing

Viable Models of Energy Metabolism: Contemplating Uncertainty in Measured Data, Parameter Estimates and Predictions

Hettling, J., 2014

Research output: PhD ThesisPhD Thesis - Research VU, graduation VUAcademic

Open Access
File
2013

Ancient Dispersal of the Human Fungal Pathogen Cryptococcus gattii from the Amazon Rainforest

Hagen, F., Ceresini, P. C., Polacheck, I., Ma, H., van Nieuwerburgh, F., Gabaldón, T., Kagan, S., Pursall, E. R., Hoogveld, H. L., van Iersel, L. J. J., Klau, G. W., Kelk, S. M., Bartlett, K. H., Stougie, L., Voelz, K., Pryszcz, L. P., Castañeda, E., Lazera, M., Mey, W., Deforce, D. & 4 othersMeis, J. F., May, R. C., Klaassen, C. H. W. & Boekhout, T., 2013, In : PLoS ONE. 8, 8, p. e71148 14 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Cryptococcus gattii
Pathogens
Amazonia
Disease Outbreaks
Animals

A Protein Prioritization Approach Tailored for the FA/BRCA Pathway

Haitjema, A., Brandt, B. W., Ameziane, N., May, P., Heringa, J., de Winter, J. P., Joenje, H. & Dorsman, J. C., 2013, In : PLoS ONE. 8, 4, e62017.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Fanconi Anemia
prioritization
Fanconi Anemia Complementation Group Proteins
Genes
Proteins

A Realistic Model under which the Genetic Code is Optimal

Buhrman, H., van der Gulik, P. T. S., Klau, G. W., Schaffner, C., Speijer, D. & Stougie, L., 2013, In : Journal of Molecular Evolution. 77, 4, p. 170-184

Research output: Contribution to JournalArticleAcademicpeer-review

Genetic Code
genetic code
Amino Acids
amino acids
amino acid

A vision and strategy for the virtual physiological human: 2012 update

Hunter, P., Chapman, T., Coveney, P. V., De Bono, B., Diaz, V., Fenner, J., Frangi, A. F., Harris, P., Hose, R., Kohl, P., Lawford, P., McCormack, K., Mendes, M., Omholt, S., Quarteroni, A., Shublaq, N., Skår, J., Stroetmann, K., Tegner, J., Thomas, S. R. & 4 othersTollis, I., Tsamardinos, I., van Beek, J. H. G. M. & Viceconti, M., 2013, In : Interface Focus. 3, 2, p. 20130004 20130004.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Industry
Profitability
Innovation
Communication
Information Science

Bioinformatics and systems biology: bridging the gap between heterogeneous student backgrounds

Abeln, S., Molenaar, D., Feenstra, K. A., Hoefsloot, H. C., Teusink, B. & Heringa, J., Sep 2013, In : Briefings in bioinformatics. 14, 5, p. 589-98 10 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Systems Biology
Bioinformatics
Computational Biology
Students
Teaching

Building Exceutable Biological Pathway Models Automatically from BioPAX

Willemsen, T., Feenstra, K. A. & Groth, P. T., 2013, 3rd International Workshop on Linked Science 2013—Supporting Reproducibility, Scientific Investigations and Experiments (LISC2013). Sydney

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademicpeer-review

Building executable biological pathway models automatically from BioPAX

Willemsen, T., Feenstra, A. & Groth, P., 2013, In : CEUR Workshop Proceedings. 1116, p. 2-14 13 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Petri nets
Semantics
Availability
Molecules

Charge group partitioning in biomolecular simulation

Canzar, S., El-Kebir, M., Pool, R., Elbassioni, K., Malde, A. K., Mark, A. E., Geerke, D. P., Stougie, L. & Klau, G. W., 2013, In : Journal of Computational Biology. 20, 3, p. 188-198

Research output: Contribution to JournalArticleAcademicpeer-review

Hardness
Partitioning
Charge
Force Field
Molecules

Computational estimation of tricarboxylic acid cycle fluxes using noisy NMR data from cardiac biopsies

Hettling, H., Alders, D. J., Heringa, J., Binsl, T. W., Groeneveld, A. B. J. & van Beek, J. H. G. M., 2013, In : BMC Systems Biology. 7, p. 82 12 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Citric Acid Cycle
Nuclear Magnetic Resonance
Biopsy
Cardiac
Magnetic Resonance Spectroscopy

CSA: Comprehensive comparison of pairwise protein structure alignments

Wohlers, I., Malod-Dognin, N., Andonov, R. & Klau, G. W., 2013, In : Nucleic Acids Research. 40, p. 303-309

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File

Current composite-feature classification methods do not outperform simple single-genes classifiers in breast cancer prognosis

Staiger, C., Cadot, S., Györffy, B., Wessels, L. F. A. & Klau, G. W., 2013, In : Frontiers in Genetics. 4, 289

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Breast Neoplasms
Genes
Boidae
Gene Expression
Gene Regulatory Networks

DALIX: Optimal DALI protein structure alignment

Wohlers, I., Andonov, R. & Klau, G. W., 2013, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 10, p. 26-36

Research output: Contribution to JournalArticleAcademicpeer-review

Protein Structure
Alignment
Proteins
Scoring
Distance Matrix

Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model

Bonzanni, N., Garg, A., Feenstra, K. A., Schütte, J., Kinston, S. J., Miranda-Saavedra, D., Heringa, J., Xenarios, I. & Göttgens, B., 1 Jul 2013, In : Bioinformatics. 29, 13, p. i80-8

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Stem Cells
Regulatory Networks
Dynamic Networks
Hematopoietic Stem Cells
Stem cells

HIV-1 envelope glycoprotein signatures that correlate with the development of cross-reactive neutralizing activity

van den Kerkhof, T. L. G. M., Feenstra, K. A., Euler, Z., van Gils, M. J., Rijsdijk, L. W. E., Boeser-Nunnink, B. D., Heringa, J., Schuitemaker, H. & Sanders, R. W., 2013, In : Retrovirology. 10, p. 102

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
HIV-1
Glycoproteins
Glycosylation
Neutralizing Antibodies
env Gene Products

HIV-1 replication fitness of HLA-B*57/58:01 CTL escape variants is restored by the accumulation of compensatory mutations in Gag

Gijsbers, E. F., Feenstra, K. A., van Nuenen, A. C., Navis, M., Heringa, J., Schuitemaker, H. & Kootstra, N. A., 2013, In : PLoS ONE. 8, 12

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Human immunodeficiency virus 1
HIV-1
mutation
Mutation
epitopes

Increased Expression of Matrix Extracellular Phosphoglycoprotein (MEPE) in Cortical Bone of the Rat Tibia after Mechanical Loading: Identification by Oligonucleotide Microarray

Reijnders, C. M. A., van Essen, H. W., van Rens, B., van Beek, J. H. G. M., Ylstra, B., Blankenstein, M. A., Lips, P. T. A. M. & Bravenboer, N., 2013, In : PLoS ONE. 8, 11, e79672.

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Microarrays
oligonucleotides
Oligonucleotide Array Sequence Analysis
tibia
Tibia

Interaction of 14-3-3 proteins with the Estrogen Receptor Alpha F domain provides a drug target interface

De Vries-van Leeuwen, I. J., da Costa Pereira, D., Flach, K. D., Piersma, S. R., Haase, C., Bier, D., Yalcin, Z., Michalides, R., Feenstra, K. A., Jiménez, C. R., de Greef, T. F. A., Brunsveld, L., Ottmann, C., Zwart, W. & de Boer, A. H., 28 May 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, 22, p. 8894-9 6 p.

Research output: Contribution to JournalArticleAcademicpeer-review

14-3-3 Proteins
Estrogen Receptor alpha
Pharmaceutical Preparations
Dimerization
Breast Neoplasms

Mapping proteins in the presence of paralogs using units of coevolution

El-Kebir, M., Marschall, T., Wohlers, I., Patterson, M. D., Heringa, J., Schönhuth, A. & Klau, G. W., 2013, In : BMC Bioinformatics. 14, Suppl. 15, p. S18

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access

RECONSTRUCTING A CORE REGULATORY NETWORK MODEL FOR BLOOD STEM/PROGENITOR CELLS

Schuette, J., Bonzanni, N., Kinston, S. J., Lelieveld, S. H., Moignard, V., Heringa, J., Feenstra, A. & Gottgens, B., Aug 2013, In : Experimental Hematology. 41, 8, p. S68-S68

Research output: Contribution to JournalArticleAcademicpeer-review

Reconstructing consensus Bayesian network structures with application to learning molecular interaction networks

Fröhlich, H. & Klau, G. W., 2013, German Conference on Bioinformatics. Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik, p. 46-55

Research output: Chapter in Book / Report / Conference proceedingConference contributionAcademic

Molecular interactions
Bayesian networks
Cutoff frequency
Linear programming
Availability

The generalized Robinson-Foulds metric

Böcker, S., Canzar, S. & Klau, G. W., 2013, In : Lecture Notes in Computer Science. 8126, p. 156-169

Research output: Contribution to JournalArticleAcademicpeer-review

2012

A critical evaluation of network and pathway based classifiers for outcome prediction in breast cancer

Staiger, C., Cadot, S., Kooter, R., Dittrich, M., Müller, T., Klau, G. W. & Wessels, L. F. A., 2012, In : PLoS ONE. 7, 4, p. e34796

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
File
breast neoplasms
Classifiers
Genes
Breast Neoplasms
prediction

A general secretion signal for the mycobacterial type VII secretion pathway

Daleke, M. H., Ummels, R., Bawono, P., Heringa, J., Vandenbroucke-Grauls, C. M. J. E., Luirink, S. & Bitter, W., 2012, In : Proceedings of the National Academy of Sciences of the United States of America. 109, 28, p. 11342-11347

Research output: Contribution to JournalArticleAcademicpeer-review

Secretory Pathway
Virulence Factors
Proteins
Mycobacterium
Site-Directed Mutagenesis

A Lagrangian Relaxation Approach to the de novo Peptide Sequencing Problem

Andreotti, S., Klau, G. W. & Reinert, K., 2012, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 9, 2, p. 385-394

Research output: Contribution to JournalArticleAcademicpeer-review

Lagrangian Relaxation
Peptides
Sequencing
Linear Programming
Scoring

An integer linear programming approach for finding deregulated subgraphs in regulatory networks

Backes, C., Rurainski, A., Klau, G. W., Müller, O., Stöckel, D., Gerasch, A., Küntzer, J., Maisel, D., Ludwig, N., Hein, M., Keller, A., Burtscher, H., Kaufmann, M., Meese, E. & Lenhof, H-P., 2012, In : Nucleic Acids Research. 40, 6, p. 1-13

Research output: Contribution to JournalArticleAcademicpeer-review

Open Access
Linear Programming
Epithelial Cells
Mutation
Heat-Shock Proteins
Cell Survival

CLEVER: Clique-Enumerating Variant Finder

Marschall, T., Costa, I., Canzar, S., bauer, M., Klau, G. W., Schliep, A. & Schönhuth, A., 2012, In : Bioinformatics. 28, 22, p. 2875-2882

Research output: Contribution to JournalArticleAcademicpeer-review

Medical Genetics
Clique
Genome
Deletion
Sequencing

Comparing clustering and pre-processing in taxonomy analysis.

Bonder, M. J., Abeln, S., Zaura, E. & Brandt, B. W., 2012, In : Bioinformatics. 28, 22, p. 2891-2897

Research output: Contribution to JournalArticleAcademicpeer-review

Taxonomies
Taxonomy
Cluster Analysis
Preprocessing
Clustering

Enabling grand-canonical Monte Carlo: extending the flexibility of GROMACS through the GromPy python interface module

Pool, R., Heringa, J., Hoefling, M., Schulz, R., Smith, J. C. & Feenstra, K. A., 5 May 2012, In : Journal of Computational Chemistry. 33, 12, p. 1207-14 8 p.

Research output: Contribution to JournalArticleAcademicpeer-review

Python
Canonical Ensemble
Molecular dynamics
Flexibility
Module